chr6-166172190-A-T

Position:

• chr6-166172190-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.13 in 151,966 control chromosomes in the GnomAD database, including 1,702 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19699 AN: 151848 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.130 AC: 19711 AN: 151966 Hom.: 1702 Cov.: 32 AF XY: 0.133 AC XY: 9897 AN XY: 74274

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0773

Gnomad4 OTH AF: 0.122

Alfa AF: 0.113 Hom.: 138

Bravo AF: 0.132

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.93

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1001978; hg19: chr6-166585678;